Abstract The 2015–2016 El Niño provided insight into how low-inflow estuaries might respond to future climate regimes, including high sea levels and more intense waves. High waves and water levels coupled with low rainfall along the Southern California coastline provided the opportunity to examine how extreme ocean forcing impacts estuaries independently from fluvial events. From November 2015 to April 2016, water levels were measured in 13 Southern California estuaries, including both intermittently closed and perennially open estuaries with varying watershed size, urban development, and management practices. Elevated ocean water levels caused raised water levels and prolonged inundation in all of the estuaries studied. Water levels inside perennially open estuaries mirrored ocean water levels, while those inside intermittently closed estuaries (ICEs) exhibited enhanced higher-high water levels during large waves, and tides were truncated at low tides due to a wave-built sand sill at the mouth, resulting in elevated detided water levels. ICEs closed when sufficient wave-driven sand accretion formed a barrier berm across the mouth separating the estuary from the ocean, the height of which can be estimated using estuarine lower-low water levels. During the 2015–2016 El Niño, a greater number of Southern California ICEs closed than during a typical year and ICEs that close annually experienced longer than normal closures. Overall, sill accretion and wave exposure were important contributing factors to individual estuarine response to ocean conditions. Understanding how estuaries respond to increased sea levels and waves and the factors that influence closures will help managers develop appropriate adaptation strategies.

Lagoon systems are more heavily impacted by hurricanes, whereas the relevant storm surge modeling studies have been paid little attention to lagoon systems and the storm-induced exchange in lagoon systems is even less understood. To address this gap, a three-dimensional unstructured grid-based model was configured for the Maryland Coastal Bays, a typical lagoon system with two unique inlets (Ocean City Inlet (OCI) and Chincoteague Inlet (CI)), to investigate how Hurricane Sandy impacted inlet dynamics. A nesting model framework was applied to provide the necessary remote forcing from a large model domain and maintain the intricate shoreline and bathymetry of an inner model domain. Results indicated that the flux patterns varied in response to the change in wind direction and rising/falling high water levels from the coastal ocean, rather than a single flow pattern during the passage of Sandy. From October 29 05:00 to 17:00 UTC, mild (> 10 m/s) and strong (> 15 m/s) northerly winds accompanied by the rising high water level from the coastal ocean promoted a mean inflow pattern at the OCI and a mean outflow pattern at the CI. Strong southwesterly winds (> 15 m/s) dominated in the bays from October 30 03:00 to 15:00 UTC. Under strong southwesterly winds and falling high water levels from the coastal ocean, flux was transported landward at the CI and seaward at the OCI. Sensitivity experiments on various storm temporal scales showed that a net inflow pattern occurred in the bays, and the net exchange amounts became smaller in response to longer storm durations. Residual effect of relatively high river flow from Sandy could still influence the salinity at the OCI, whereas the CI salinity was not affected by river flow owing to a long distance between the CI and river locations.

Abstract High-resolution satellite imaging represents a potentially effective technique to monitor cyclone-caused environmental damage and recovery over large areas at a high spatial scale. This study utilized a 10-m resolution Sentinel satellite image series to document vegetation changes in a portion of the Florida Keys, USA, over which the core of Category 4 Hurricane Irma passed on 10 September 2017. A previously assembled field survey was used to establish land-cover patterns in the satellite data, and concurrent field measurements verified post-hurricane changes. Normalized difference vegetation index (NDVI) was utilized as a tracer for pre-storm baseline patterns and through 19 post-storm months. NDVI patterns show that the severity of vegetation damage varied appreciably across the area, with the least damage on islands in the western sector of the hurricane’s eye and around its center, and greatest damage on islands just east of the eye. The data reveal that for 2.5 months after the storm, multiple inland vegetation classes showed substantial early regrowth. However, mangrove forests were more negatively affected. The storm caused extensive mortality of black mangrove (Avicennia germinans) and red mangrove (Rhizophora mangle), corresponding to more than 40% of the total mangrove area on some islands. The full extent of mangrove die-off was not immediately evident, and increased progressively through the first few months after the storm. In addition to demonstrating the utility of high-resolution satellite image series for post-hurricane environmental assessment, this study reveals high-resolution links between vegetation types, their location within the cyclone, and the extent of post-storm recovery.

Many studies have evaluated the impacts of hurricanes on coral communities, but far less is known about impacts, recovery, and resilience of sponge communities to these extreme events. In September 2017, St. Thomas, U.S. Virgin Islands, was impacted by two Category 5 hurricanes within 2 weeks: Hurricanes Irma and Maria. Such extreme events occurring in such rapid succession are virtually unprecedented. Pre-hurricane (2015, 2016) surveys of permanent transects at six sites around St. Thomas were compared with those at 10 weeks post-hurricanes (December 2017) to evaluate storm impacts on sponges and on benthic coral reef constituents. These surveys also established a baseline for evaluating future recovery. Percent cover of sponges declined by 24.9% post-hurricanes. In contrast, sponge density increased by 43.9% from 2015 to 2016 and declined slightly after the hurricanes. Overall sponge volume did not vary over time, and whereas sponge diversity was similar in 2015 and 2016, it increased post-hurricanes. Sponge morphologies were differentially affected by the hurricanes; the proportion of upright sponges declined by 36.9%, while there was a 24.4% increase in encrusting sponges. Coral and macroalgal cover did not change significantly over the sampling period, while percent cover of epilithic algae increased and non-living substrata decreased from 2015 to 2016 but did not change further post-hurricanes. At all sites, recruitment and/or regrowth of sponges was observed within 10 weeks post-hurricanes, indicating potential resilience in Caribbean sponge communities. Whether these sponge communities return to pre-hurricane conditions and how long that will take remains to be seen.

Regional approaches to coastal wetland restoration are one of the best ways to ensure that these threatened habitats persist in the face of sea level rise. Regional approaches provide a mechanism for prioritizing restoration actions in areas where future conditions will promote maximum resiliency while still providing for an appropriate composition of plant and animal habitats across the region as a whole. Developing a regional restoration strategy requires understanding historical losses relative to contemporary habitat distributions, predicting future changes due to sea level rise (and other stressors), and evaluating management actions with the potential to offset expected future losses. In this study, we present an approach to assess historical losses and future management options for more than 100 individual wetlands along the Southern California (USA) coast ranging in size from a few tenths of a hectare to over 250 ha. This analysis was conducted to support development of a regional wetland strategy that will guide restoration in Southern California for the next several decades. The approach consisted of reconstructing historical wetland distribution using US Coast and Geodetic Survey T-sheets, mapping current wetlands and classifying them into archetypes that represent different settings and processes, and predicting future distributions based on a hypsometric model of elevation changes under various sea level rise and management scenarios. Historical analysis revealed that two-thirds of the 331 wetlands present in ca. 1850 and 75% of vegetated estuarine habitat area has been lost, with most losses occurring in small to medium size wetlands. Up to 69% of the remaining marshes and flats could be lost with 1.7 m of sea level rise, with an associated increase in subtidal habitat. However, potential future losses could be largely offset, and total area could increase under scenarios of facilitated wetland migration and sediment augmentation. Although the future distribution of wetlands would likely be different from current conditions, sufficient habitat would be provided region-wide. This analysis demonstrates how regional analysis of historic, present, and likely future conditions can support a strategy that could lead to net wetland gain under future sea level rise conditions. However, immediate and decisive action is necessary.

Abstract Arctic calcifiers are believed to be particularly vulnerable to ocean acidification as the Arctic already experiences low carbonate saturations states due to low temperature and high inputs of freshwater. Here, we report the finding of dense beds of Mytilus growing in tidal lagoons and river mouths, where the availability of carbonate ions is remarkably low Ωarag < 0.5. Although these Mytilus grow in the intertidal zone, and therefore are covered by seawater during high tide, δ18O isotopes of shell carbonate were low − 2.48 ± 0.05‰, confirming that their shells were deposited under low salinity conditions, i.e., reflecting a contribution from 18O-depleted freshwater. δ18O isotopes of shell carbonate became heavier with increasing salinity, with mean values of − 0.74 ± 0.96‰ for Mytilus growing in tidal pools. We calculated, based on δ18O isotopic composition standardized to a common temperature, that freshwater accounted for 7% of the carbonate oxygen in the shells of Mytilus at the habitats with near full-strength seawater salinity compared with 25% in shells collected at sites temporarily exposed to freshwater. The composition of the periostracum revealed a trend for shells from river mouths and brackish tidal lagoons to be more depleted in polysaccharides than shells exposed to higher salinity. We conclude that the high food supply associated with riverine discharge allows Mytilus to cope with the low saturation states by using energy to calcify and modify their periostracum to protect the shells from dissolution. These findings suggest that Arctic Mytilus are highly resistant to low saturation states of carbon minerals if supplied with sufficient food.

Salinity is a limiting factor for many invertebrates, especially for Odonata which are typically associated with freshwater ecosystems. In Europe, 15 Odonata species inhabit brackish wetlands and only few detailed data on their tolerance towards salinity are available. We investigated Odonata fauna in 11 sampling stations situated in three estuarine areas (northern Adriatic coastline) which differed in salinity conditions (freshwater- polyhaline habitats) in order to assess affinity of Odonata species to brackish habitats and to describe their distribution pattern in coastal wetlands. Adults, exuviae (the remains of the exoskeleton after the last larval instar), and the main chemical and physical water parameters were sampled every 2 weeks for 1 year in each station. In total, 25 species were detected and 56% of them were able to complete their life cycle in brackish water environments. Our results showed that freshwater and oligohaline ponds were the most favorable for dragonflies, with an overall higher species richness. There was a high species turnover along the salinity gradient, with a strong differentiation among the communities along the gradient. Considering the exuviae, we observed a high specificity with respect to the habitat conditions (seven species exclusive of freshwater sites and six of oligohaline ones, respectively). Among the adults, four species were found exclusively in freshwater habitats and no species seemed to be strictly connected with oligohaline habitats. Coastal wetlands are composed by a mosaic of different habitats especially when freshwater and seawater are close together, supporting many Odonata species with different tolerance toward salinity conditions. They also provide useful insights for conservation and management actions.

Coincidental long-term changes in estuarine nekton assemblages and environmental conditions are widely reported. In this study, from a warm-temperate, high salinity, salt marsh-dominated estuary in the southeastern USA, decreases in overall abundance, shifts in species and life stage composition, and changes in seasonal patterns of occurrence coincided with increased water temperature. Biweekly trawl collections in a subtidal creek were made during two 4-year periods separated by more than 30 years. Of the total 111 taxa in the North Inlet estuary, South Carolina, 64% (71) occurred during both the historic (1981–84) and recent (2013–16) periods. The top five species and their proportions of the total annual catches changed between periods. In the recent study period, near-bottom species (Lagodon rhomboides, Bairdiella chrysoura, Litopenaeus setiferus) increased, and pelagic species (Anchoa spp. and Lolliguncula brevis) decreased. The mean abundance of total nekton in the recent period was approximately 50% of historic abundance. Large, but temporary increases in nekton abundance occurred when salinity decreased after major storms. In the recent study period, shifts in the timing of peak abundances from spring to fall, the occurrence of juveniles during winter, and increased diversity suggested responses to significantly warmer winters and summers. Over the 30 year period, the subtidal nekton assemblage transitioned to a state of lower abundance and different composition. Future increases in water temperature, incidences of major storms, and modifications of estuarine habitats due to rising sea level could lead to additional changes in the fauna of warm-temperate estuaries.

Abstract To clarify the effects of crab burrows on variation in sediment CO2 flux in mangrove forest, we measured the traits of crab burrows (density and entrance area size) and the CO2 flux rate from sediment surfaces, in areas with and without burrows, in a subtropical mangrove forest on Ishigaki Island, southwestern Japan. Burrow density and entrance area showed significant differences among seasons (warm, middle, and cool) and mangrove zones (upper-, middle-, and downstream), which may have depended on crab phenology, life cycle, and species composition. The sediment CO2 flux rate was significantly higher at plots with crab burrows (B+) than at those without burrows (B−) in each zone and season. However, standardized sediment CO2 flux rate by burrow surface area at B+ plots did not differ significantly from that at B− plots. In addition, there were no significant differences in sediment temperature and sediment water content between the two types of plots. Moreover, the level of microbial respiration differed significantly between sediments collected from the deep part and those collected from either the ground surface part or burrow walls. These results suggest that crab burrows increase sediment CO2 flux from the mangrove forest floor by increasing the sediment–atmosphere interface area, thereby inducing a change to aerobic conditions in the sediments around burrows. Therefore, the seasonal and spatial effect of crab burrows on the forest floor should be considered when evaluating sediment CO2 flux and examining the role of the mangrove ecosystem as a carbon sink.

Geochemical signals in bivalve carbonate hold the potential to record environmental change over timescales from months to centuries; however, not all bivalves provide reliable proxy records, and modern studies are essential to calibrate these relationships prior to use in palaeo-environmental reconstruction. In this study, 19 shells of the estuarine bivalve Arthritica helmsi, from 14 sites in Southeastern Australia, were obtained from museum collections and analysed for trace elemental (Sr/Ca, Mg/Ca, Sr/Li and Ba/Ca) and stable isotopic ratios (18O/16O and 13C/12C). Mean Sr/Ca and Mg/Ca exhibited significant negative correlations to temperature (R2 = 0.49, p = 0.001; R2 = 0.25, p = 0.02) in agreement with previously published models for trace element partitioning into inorganic aragonite. In addition, the within-shell range of Sr/Ca and Mg/Ca, as measured by laser ablation ICP-MS, correlated to the temperature range (R2 = 0.22, p = 0.03; R2 = 0.46, p = 0.002, respectively). Sr/Li ratios were also negatively correlated to temperature (R2 = 0.34, p = 0.008); however, a significant difference in the model coefficients with previous studies indicates this proxy should be applied with caution. Both oxygen and carbon isotope values exhibited large differences between shells from terrestrial, estuarine and marine waters, suggesting that these stable isotopes hold a potential to record large environmental changes such as sea-level changes or freshening/salinisation in estuarine environments. This study presents the first geochemical study of Arthritica helmsi, highlighting its potential as an environmental tracer.

Abstract The Tarium Niryutait Marine Protected Area within the Mackenzie Estuary provides a critical summer habitat for the Eastern Beaufort Sea (EBS) beluga whales (Delphinapterus leucas). Given the lack of seabed characterization in the Mackenzie Estuary, there is a need to characterize key features and governing processes that may influence or drive beluga habitat use. Thus, we sample and describe the Mackenzie Estuary seabed and examine the influence of ice conditions, fluvial processes and wave interactions to define seabed processes and spatially defined habitats. Lastly, we examine how beluga selects specific seabed characteristics or habitat types. Seabed mapping, sediment sampling and delineation of seafloor features are used to define the seabed habitat. The majority of the seabed consists of medium to coarse-grained silt and is void of any bathymetric variations and disturbances. Five seabed habitat zones were defined: (1) featureless and flat, (2) scours and disturbed, (3) sandy shoal, (4) deep channel and (5) longshore bars. Beluga observations analysed retrospectively from 1972 to 1992 were associated with the featureless and flat seabed habitat 72% of the time. However, a preference for the sandy shoal habitat provides some indication there are substrates in the estuary which are suitable for whales to rub against (to scrape off moulting skin), supporting the hypothesis there are certain habitats that may attract belugas during the annual moult.

Abstract Mangroves store large amounts of organic carbon (C) in their soils and are important in the global C cycle. These C stocks have been attributed to the below-ground productivity of mangroves, yet there is limited knowledge about the environmental factors that influence mangrove root growth. Thus, this study aimed to assess the role of variation in soil bulk density (BD) on the early development of mangroves. Seedlings of four mangrove species were grown in a pot-experiment in soils with a BD ranging from 0.2 to 1.2 g cm−3. Nine functional above- and below-ground plant traits were measured. Above- and below-ground traits of mangrove seedlings were influenced by variation in soil BD, but the effect was species specific. The reaction norms for most plant traits of Bruguiera gymnorrhiza and Rhizophora stylosa suggested a growth optimum at a specific soil BD (0.6 and 0.4 g cm−3, respectively), whilst the reaction norm of Avicennia marina was highly variable among traits, and Ceriops australis showed a very limited response. Moreover, A. marina was the most plastic species above-ground, while R. stylosa was the most plastic species below-ground. Ceriops australis was the least plastic species. Hence, soil BD is an environmental factor that influences mangrove root traits and seedling establishment, and may therefore affect mangrove species distributions and ecosystem C stocks.

Abstract Juvenile American shad (Alosa sapidissima) experience a wide range of temperatures in rivers before migrating to the ocean. Temperatures in these freshwater environments can vary greatly spatially, seasonally, year-to-year, and can be impacted by anthropogenic factors such as power plant discharge or climate change. Currently, there is uncertainty concerning juvenile American shad thermal tolerance due to a lack of a well-controlled study. Here, we report results of laboratory experiments to establish the upper thermal tolerance and heat shock protein response of juvenile American shad exposed to gradually increasing temperatures. Upper thermal tolerance was determined to be 35 °C (median; range = 34–36 °C) when fish were acclimated to 25 °C and temperatures were raised 1 °C day−1. Heat shock protein response was indicated by changes in branchial mRNA abundance of the inducible heat shock protein 90 alpha (hsp90α), which was significantly elevated (more than 5-fold increase) at 30 °C, and highest in fish that had reached their upper thermal maximum between 34 and 36 °C. Our findings indicate a higher upper thermal tolerance than previously reported for juvenile American shad, and an onset temperature of hsp90α induction at 30 °C, a temperature juvenile American shad commonly experience during summer months.

Eutrophication is a challenge to coastal waters around the globe. In many places, nutrient reductions from land-based sources have not been sufficient to achieve desired water quality improvements. Bivalve shellfish have shown promise as an in-water strategy to complement land-based nutrient management. A local-scale production model was used to estimate oyster (Crassostrea virginica) harvest and bioextraction of nitrogen (N) in Great Bay Piscataqua River Estuary (GBP), New Hampshire, USA, because a system-scale ecological model was not available. Farm-scale N removal results (0.072 metric tons acre−1 year−1) were up-scaled to provide a system-wide removal estimate for current (0.61 metric tons year−1), and potential removal (2.35 metric tons year−1) at maximum possible expansion of licensed aquaculture areas. Restored reef N removal was included to provide a more complete picture. Nitrogen removal through reef sequestration was ~ 3 times that of aquaculture. Estimated reef-associated denitrification, based on previously reported rates, removed 0.19 metric tons N year−1. When all oyster processes (aquaculture and reefs) were included, N removal was 0.33% and 0.54% of incoming N for current and expanded acres, respectively. An avoided cost approach, with wastewater treatment as the alternative management measure, was used to estimate the value of the N removed. The maximum economic value for aquaculture-based removal was $105,000 and $405,000 for current and expanded oyster areas, respectively. Combined aquaculture and reef restoration is suggested to maximize N reduction capacity while limiting use conflicts. Comparison of removal based on per oyster N content suggests much lower removal rates than model results, but model harvest estimates are similar to reported harvest. Though results are specific to GBP, the approach is transferable to estuaries that support bivalve aquaculture but do not have complex system-scale hydrodynamic or ecological models.

We examined the effects of passive integrated transponder (PIT) tags on the survival, growth, and tag retention for two common estuarine fishes, mummichog (Fundulus heteroclitus) and pinfish (Lagodon rhomboides). A separate laboratory experiment was conducted for each species where individuals, ranging in initial size from 45 to 82 mm standard length (SL), were implanted with 8-mm or 12-mm PIT tags. Across both experiments, the probability of survival for tagged individuals ranged from 82 to 92%, probability of tag retention ranged from 82 to 91%, and probability of survival and tag retention ranged from 73 to 83%. For both species, most mortality and tag loss occurred for small (< 60 mm) individuals tagged with 12-mm tags, and generally early in the experiments. There was little effect of tagging on growth for individuals of either species compared to individuals in untagged control treatments. We recommend a minimum length of 55 mm SL for mummichog and 65 mm SL for pinfish when tagging with 8-mm or 12-mm PIT tags, as almost all fishes above these sizes survived and retained their tags. Direct comparison of our results with other studies was difficult because of variation in the tagging, husbandry, and experimental protocols used in experiments. A comparison among these different protocols would be useful to determine the least intrusive, most effective, and optimal procedure for a given species or group of estuarine fishes.

Estimates of the types and number of recreational users visiting an estuary are critical data for quantifying the value of recreation and how that value might change with variations in water quality or other management decisions. However, estimates of recreational use are minimal and conventional intercept survey methods are often infeasible for widespread application to estuaries. Therefore, a practical observational sampling approach was developed to quantify the recreational use of an estuary without the use of surveys. Designed to be simple and fast to allow for replication, the methods involved the use of periodic instantaneous car counts multiplied by extrapolation factors derived from all-day counts. This simple sampling approach can be used to estimate visitation to diverse types of access points on an estuary in a single day as well as across multiple days. Evaluation of this method showed that when periodic counts were taken within a preferred time window (from 11 am–4:30 pm), the estimates were within 44% of actual daily visitation. These methods were applied to the Three Bays estuary system on Cape Cod, USA. The estimated combined use across all its public access sites is similar to the use at a mid-sized coastal beach, demonstrating the value of estuarine systems. Further, this study is the first to quantify the variety and magnitude of recreational uses at several different types of access points throughout the estuary using observational methods. This work can be transferred to the many small coastal access points used for recreation across New England and beyond.

Estuarine and coastal marine ecosystems can have significant intra- and interannual variability in faunal community structure, complicating management response to disturbances as disturbance effects must be detectable within normal variability and on timescales relevant to management entities. We examined a long-term, multi-gear dataset on estuarine faunal (fish and select invertebrate) communities to determine if community structure changes due to disturbances could be detected on management-relevant timescales (e.g., years), given that these communities have known seasonal and interannual variability. Results from multivariate, community-based analyses, and several univariate diversity indices for fauna of Tampa Bay, Florida, USA suggested general community stability over the long term, with the exceptions of 2005–2006 (prolonged red tide event) and 2010 (extreme cold event in winter). Community structure was notably outside the typical variability for both time periods. In 2005, species richness decreased by half for one gear type and was the lowest on record for the other two gear types. In 2010, when the relative abundance of a top predator decreased by 50% from cold-related mortality, Simpson’s diversity index was the lowest on record for one gear type. The red tide and extreme-cold events differed in duration and the number of taxa directly impacted (multispecies vs. single-species, respectively) but both multivariate and univariate analyses indicated significant deviation in the faunal community structure during these years. Within 1–3 years after these major events, however, the community seemed to have returned to a structure like that of previous years, suggesting long-term stability and resilience. Our results confirm that multivariate and univariate analyses can detect major disturbances to estuarine faunal communities, which gives management entities options for which analysis approach is appropriate for their needs. Since the Tampa Bay faunal communities recovered within 3 years, we suggest that where long-term monitoring exists, active restoration might be deferred while monitoring for signs of recovery following the removal of a perturbation. This is a fundamental part of sound adaptive management processes to promote sustainable ecosystems.

Category five hurricanes Irma and María (September 2017) caused significant damage to shallow seagrass communities across Puerto Rico. The magnitude and spatial extent of hurricane impacts on representative seagrass habitats of Culebra Island were addressed using a combination of random photo-quadrats and before–after hurricanes GIS-based imagery analyses. There was a significant loss of shallow seagrasses across all nine surveyed locations. Most of the documented impacts were associated with sediment bedload (horizontal transport), which resulted in burial and suffocation. There was also localized physical disruption of the seagrass habitat matrix across locations exposed to stronger wave action, creating major scars and exposing below-ground structure to further disintegration by future storm events. Displaced coral rubble also caused seagrass burial. Aerial imagery analyses (2007, 2010, 2017) showed a significant decline in seagrass percent cover. Seagrass decline was positively correlated with wave exposure (p < 0.05). Seagrass cover, density, and changes in benthic community structure were documented across five of the surveyed locations during 2018, and these data were further compared to data collected in 2004 at these same sites. There was a decline in percent seagrass cover and density and a change in benthic community structure favoring habitat homogenization. A remarkable finding was the rapid recovery, expansion, and increased localized dominance of the invasive seagrass, Halophila stipulacea. This was particularly evident in areas impacted by recurrent land-based runoff pulses, anchoring, sediment resuspension due to navigation, trampling or by the accumulation of decaying Sargassum mats. Hurricanes triggered a localized shift in marine vegetation, favoring the invasion of H. stipulacea, with potentially significant consequences on ecosystem resilience and on the ability of native in seagrasses to persist and adapt to projected climate change impacts.

Abstract The spatio-temporal variability of the chlorophyll-a (chl-a) concentration in the East Sea (Japan Sea) (EJS) was investigated using Moderate Resolution Imaging Spectroradiometer (MODIS) data over 13 years from 2003 to 2015 to understand the impact of physical environmental changes on low-trophic level marine ecosystems. The chl-a images were composited to produce gridded monthly chl-a images using a weighted average method after applying a speckle removal algorithm to each path image. Missing pixels without any satellite observations because of cloud coverage were objectively filled using three-dimensional optimal interpolation. The first empirical orthogonal function (EOF) mode of the monthly chl-a images, accounting for 14% of the total variance, showed higher eigenvectors values in the eastern part of the EJS and distinct annual peaks each spring. The amplitudes of the first EOF mode, despite the dominant year-to-year variations in chl-a, tended to increase during spring over time. The recent 13-year trend of chl-a showed differences between the southwestern part and the northeastern part of the EJS, and this difference clearly appeared in the monthly trend maps for March and April. The eastern coast of Korea showed a highly positive trend during summer, particularly during August. The changes in chl-a over the decade were related to the physical environmental changes in sea surface wind, mixed layer depth, and stratification of upper sea water in the EJS.

Abstract The legacy effects of mosquito ditching have made salt marshes more vulnerable to flooding impacts from climate change, presenting management challenges in New England where the majority of salt marshes have been ditched and greater rates of sea level rise and storm events are being observed. One legacy effect of mosquito ditching appears to be subsidence of the marsh, with greater effects near the ditches and extending into the marsh plain. We found an average of 9 cm subsidence midway between ditches that averaged 14 m apart. Ditch Remediation is a new approach to filling ditches that uses existing hydrology and vegetation to mend ditches from the bottom up to restore marsh plain elevations. Smaller, auxiliary ditches are selected for treatment. Hay is mown, allowed to dry, and rolled into the treatment ditch where it is held using twine. Nine ditches in four areas were treated in fall 2014 and 2015. Depth of treated ditches decreased an average of 18 cm by fall 2017, and Spartina alterniflora colonized the ditch centers (plant cover and stem density increased). It is unknown whether the trajectory of filling and revegetation of the ditches will continue on their own or if the reduction in drainage depth will stimulate marsh plain building. Ditch remediation could remove excessive drainage effects of half the ditches, thereby approaching an optimal drainage density that may allow tidal marshes to rebuild elevation. This simple and inexpensive technique to reduce ditch impacts should be considered by partnerships that include mosquito control agencies.

Abstract Several aquatic species use beach foreshores to lay their eggs. Understanding the dynamics of egg entrainment versus egg retention in foreshore sediment is important to delivering eggs to foraging species, and to predicting fecundity and population responses of beach nesting species to harvest and habitat management. Exhumation of these eggs is primarily by bioturbation and wave action. This study isolates effects of wave and swash processes on exhumation, entrainment, and transport of horseshoe crab eggs by conducting a 1-day field study designed to avoid effects of bioturbation by spawning and migratory shorebird predation. Dyed sand and horseshoe crab (Limulus polyphemus) eggs were injected into the foreshore of an estuarine beach in Delaware Bay, USA and sampled during 110 swash events using streamer traps. Significant wave heights ranged from 0.30 to 0.47 m. The quantity of eggs exhumed from the mid-foreshore by waves and swash was 3.8 times greater than from the upper foreshore where activation was by swash alone. Swash flows were skewed offshore, but egg transport was predominantly onshore from bore collapse. Egg release was greatest in early rising tide, making this the most productive time for shorebird foraging. Release of eggs from mid-foreshore may be dominated by wave action during high energy days with little spawning or by bioturbation by horseshoe crabs during intensive spawning. Activation depths in the swash were low, indicating that eggs buried on the upper foreshore can reach later stages of development after spawning ceases.

Abstract Understanding the trophic ecology of early developmental stages of commercial fish species migrating between sea and coastal lagoons is crucial to effective management of nursery habitats and resulting resources. While most information on diet shift of the gilthead seabream Sparus aurata comes from studies in experimental conditions, here we investigated the trophic niche dynamics of post-larvae, juveniles and sub-adults in natural environment, hypothesising that habitat and resources use of marine and lagoonal sites will exhibit strong relationship with ontogeny of the species. Carbon and nitrogen stable isotopes showed evidence of a clear shift in the trophic niche features, trophic position and trophic pathways supporting S. aurata during growth. Main differences occurred between post-larvae and juveniles/sub-adults, perfectly matching their diet shift from zooplanktivorous to zoobenthivorous habits. The wider trophic niche of juveniles exploiting the variety of resources within the lagoon, compared to the narrower niche of marine post-larvae demonstrates the importance of the trophic role of the lagoon as nursey ground, where aquatic macrophytes (seagrasses and macroalgae) provide the main trophic support as sources of organic matter.

Limited evidence for spatial patterns of denitrification in tidal freshwater forested wetlands (TFFWs), seemingly due to high spatial variability in the process, is surprising considering the various spatial gradients of its biogeochemical and hydrogeomorphic controls in these ecosystems. Because certain physical environmental gradients may be useful for the prediction of denitrification in TFFWs, we measured denitrification and ecosystem attributes in hummock-hollow microtopography of TFFWs along longitudinal riverine positions (upper, middle, and lower tidal river sites, and nearby upstream nontidal forested floodplains) of the adjoining Pamunkey and Mattaponi Rivers, Virginia. We tested differences by river, site, and plot in denitrification enzyme activity (DEA) and substrate limitations of denitrification potential (DP). The Pamunkey River carries greater river nitrate concentrations, and we found less nitrate limitation of DP and greater soil nitrate in hollows of this river. DEA in tidal hummocks was positively correlated with soil organic matter, nitrogen, and carbon, with the highest rates in lower tidal sites. Hummocks also promoted greater oxygen-controlled substrate limitation of DP, whereby experimental aeration stimulated DP under subsequent inundation more in hummocks than hollows. Additionally, tidal sites had greater DEA than nontidal sites, inferred to be caused by a combination of higher moisture, organic, and nutrient content. Our results indicate that the increasing nitrogen concentrations in these rivers will increase denitrification more on the Mattaponi River by alleviating its greater nitrogen limitation compared to the Pamunkey River, and modification to sedimentation, inundation, or microtopography from sea level rise may alter denitrification gradients in TFFWs and upstream low-elevation nontidal floodplains.

Abstract Accelerating losses of seagrass meadows motivate the restoration of these highly productive and beneficial ecosystems. Understanding how environmental parameters including depth and temperature affect restoration trajectories through time is key to conserving and restoring seagrass meadows. We used a long-term (12-year), landscape-scale experiment to test the effect of depth on eelgrass (Zostera marina) restoration success and resilience to a marine heat wave (MHW) disturbance. We found that depth was a critical determinant of seagrass restoration success, with no long-term success at sites deeper than 1.5 m below mean sea level (MSL) or shallower than − 0.8 m MSL. Seeds germinated below − 1.5 m MSL, but shoots did not persist, confirming earlier predictions from a hydrodynamic-vegetation model. Depth was also a significant predictor of seagrass resilience following MHW disturbance. Our results suggest that areas of restored seagrass that are resilient to temperature stress exist across an intermediate depth range, excluding the shallowest and deepest portions of the full habitable depth range for restored seagrass. Over the next decades, sea-level rise will likely affect both the habitable area and the resilient area, available for seagrass restoration. However, seagrass enhancement of sediment accretion may at least partially offset sea-level rise rates. As ocean temperatures warm and MHWs occur more frequently, the resilience of seagrass meadows to temperature stress will be of increasing concern. These results suggest that depth is a critical parameter that will help determine what areas are most resilient and therefore most suitable for conservation and restoration.

Abstract For conservation management of grassland ecosystems, an important question is under which conditions large grazers induce compositional and structural variation in plant communities, which is a prerequisite for high biodiversity. Here we used two long-term projects on the mainland salt marshes of the Wadden Sea to test the hypothesis that long-term grazing management with different stocking densities results in plant communities with distinctively different plant species composition and vegetation structure. The two projects took place on a low clayey and a high sandy salt marsh with different stocking densities of sheep: 0, 1.5, 3.5, 4.5 and the initially 10 sheep ha−1, where measurements were collected 11, 15, 19 and 23 years after the start of the project. Moreover, grazers affect abiotic conditions by reducing soil-redox potential and surface elevation, thereby driving composition and structure of salt-marsh vegetation. On the low salt marsh, a continued high stocking density (10 sheep ha−1) resulted in succession from the early-successional Puccinellia maritima community to the late-successional Atriplex portulacoides community. On the high salt marsh, the early-successional Festuca rubra community was maintained under all stocking densities. Cessation of grazing resulted in succession to the Elytrigia atherica community in both salt-marsh types. Intermediate stocking densities (1.5, 3 or 4.5 sheep ha−1) resulted in a mosaic of tall vegetation and patches of lawn, i.e. short-grazed vegetation, where Puccinellia maritima lawn occurred interspersed with patches of the Festuca rubra and tall Elytrigia atherica communities in both salt-marsh types. Effects of grazers were influenced by the presence of watering points near the sea wall. To conclude, our results show how joint interactions between grazers and abiotic conditions drive vegetation diversity and heterogeneity, with implications for ecosystem functions and services such as wildlife biodiversity and coastal protection.

In stratified estuaries susceptible to wind mixing events, the changes in stratification have important implications for estuarine dynamics. Understanding the timescale associated with these mixing events and indirect wind impacts is dependent on estimating the restratification timescale. Bay-wide stratification observations, turbulence time series, and long-term data were examined to quantify the response mechanisms and restratification times in Mobile Bay. Observations showed moderate increases in stratification occurred over 2–3 days after the mixing event and were spatially variable. Turbulence data and model results that further highlight the period of returning stratification had changes in the relative contribution of tidal straining and gravitational exchange for the residual circulation in the estuary. Estimates of dissipation for the two ADVs averaged 2.6–3.1 × 10−5 m2 s−3 prior to the mixing event and increased to 1.4–8.5 × 10−4 m2 s−3 after the mixing event. These changes showed with increasing stratification; the turbulent dissipation decreased. These results highlight initial high returns in stratification are slowed over time as the exchange and mixing in the bay develop, and stratification returns to its premixed state.

Abstract Estuaries are important conduits between terrestrial and marine aquatic systems and function as hot spots in the aquatic methane cycle. Eutrophication and climate change may accelerate methane emissions from estuaries, causing positive feedbacks with global warming. Boreal regions will warm rapidly in the coming decades, increasing the need to understand methane cycling in these systems. In this 3-year study, we investigated seasonal and spatial variability of methane dynamics in a eutrophied boreal estuary, both in the water column and underlying sediments. The estuary and the connected archipelago were consistently a source of methane to the atmosphere, although the origin of emitted methane varied with distance offshore. In the estuary, the river was the primary source of atmospheric methane. In contrast, in the adjacent archipelago, sedimentary methanogenesis fueled by eutrophication over previous decades was the main source. Methane emissions to the atmosphere from the study area were highly variable and dependent on local hydrodynamics and environmental conditions. Despite evidence of highly active methanogenesis in the studied sediments, the vast majority of the upwards diffusive flux of methane was removed before it could escape to the atmosphere, indicating that oxidative filters are presently still functioning regardless of previous eutrophication and ongoing climate change.

Abstract Salinity conditions experienced by organisms in coastal regions may shape their life histories. Here, salinity’s impact on reproduction and survival of the hydrozoan Eleutheria dichotoma was investigated using laboratory-cultured individuals originating from Banyuls-sur-Mer (southern France) collected several decades ago. During the experiment (October 2014–July 2015), hydroid colonies and medusae were exposed to three salinities (25, 35, 45). Asexually budded medusae were collected from colonies and reared for three generations obtained by asexual budding of medusae. Salinities experienced by hydroid colonies had only minor effects on initial size, time to maturity, medusa budding, sexual production of planulae by medusae, and survival. In contrast, salinities experienced by medusae influenced their life histories. Compared with medium salinity (35), low-salinity medusae (25) had an earlier onset and higher rates of asexual budding, a later onset and slower rates of sexual reproduction, and higher mortality, which could result from allocation tradeoffs. The increased production of planulae by medusae in low salinity indicated that they were transitioning to a benthic polyp life form more resistant to environmental stress. High salinity (45) delayed asexual maturity, prevented sexual maturity in medusae, and led to lower survival and asexual reproduction rates. Budding rates decreased across the generations; however, planula production rates decreased in medium salinity but increased in low salinity. This might be explained by the accumulation of damage with each generation, and/or by internal rhythms. The flexible responses of this tractable model organism, Eleutheria dichotoma, to salinity change may be useful in future studies on changing estuarine conditions.

Abstract Eelgrass (Zostera marina L.), an underwater marine flowering plant, has a high degree of morphological plasticity that allows it to survive and adapt to environmental changes. To test the effect of eelgrass genetic diversity (measured as allelic richness and observed heterozygosity) on resilience to stresses associated with eutrophication, eelgrass from ten genetically differentiated populations was studied in outdoor mesocosms. In a full factorial experiment lasting 3 months, eelgrass was subjected to two light levels (100 and 58% ambient) and two sediment treatments (1 and 8% organic content). Some populations of eelgrass showed higher resilience, measured as a combination of productivity and survival, when exposed to the stress of high sediment organic matter and, to a lesser extent, reduced light. Overall, eelgrass resilience correlated positively with eelgrass source population genetic diversity. The findings show that eelgrass resilience to stress typical of eutrophic estuaries (low light, high organic sediment) is improved by genetic diversity, with implications for transplantation, conservation, and management.

Together, macroalgal tissue biochemical nitrogen indices (N-indices) and macroalgal abundance can be used as bioindicators of N-enrichment in estuaries. In this study, we examine the extent and rates of response of Ulva bioindicators during rapid N-enrichment perturbations in the eutrophic Avon-Heathcote Estuary (AHE) (Christchurch, New Zealand). With the diversion of the city’s wastewater discharge away from the estuary in March 2010, a ~ 90% reduction in the estuary’s N-concentration was expected. In turn, this was expected to reduce macroalgal biomass and improve the overall trophic condition of the estuary. We surveyed Ulva bioindicators over a five-year period spanning the diversion. There was a rapid (within one year) transition away from eutrophic condition reflected in N-indices (tissue-chlorophyll, -free amino acids, -N and -δ15N) following wastewater diversion, towards values corresponding with ‘cleaner’ water quality. This was accompanied by large reductions in Ulva percent cover, based on seasonal surveys conducted from 2001 to 2014. However, two large earthquakes in February and June 2011 caused a breakdown of the city’s wastewater infrastructure, resulting in overflows of untreated sewage into the estuary between February and November 2011. The re-enrichment of N and changes in N-sources (treated versus untreated sewage) were rapidly reflected in Ulva bioindicators, notably δ15N. Following repair of infrastructure, Ulva bioindicators again reverted towards a less eutrophic state. Overall, bioindicators were sensitive to changes in N-availability and N-source, and useful for identifying the position of algal populations on a eutrophic-to-oligotrophic gradient. These attributes demonstrated their utility as adjuncts to water quality monitoring and algal biomass surveys.

In the original version of the article there was an error during the production of Fig. 3.

Blennies and gobies are among the most abundant fishes in western Atlantic and Gulf of Mexico estuaries. They establish nests and maintain territories in oyster reefs and around other shallow-water structures during warm months. In this study, site fidelity and movements were determined for adult striped blenny, naked goby, freckled blenny, crested blenny, and feather blenny, in descending order of abundance. Recaptures among 221 tagged fishes at nine intertidal oyster reefs in a southeastern U.S. saltmarsh estuary provided information about fidelity for individual oyster reefs and nest sites as well as the size of territories (areas used) around nest sites. An overall recapture rate of 94% for fishes on reefs where they were tagged indicated high fidelity. Total recapture rates for the four blenny species ranged from 38 to 50%, but the naked goby recapture rate was only 9%. Within a breeding season, fidelity for specific nest sites was 58% for all blennies and 17% for gobies. Movements away from nest sites were limited with 56% of all fishes re-occurring ≤ 1 m from the original tagging site. Territories of < 5 m were identified for > 84% of the recaptured fishes. Differences in species composition and abundance between reefs suggested species-specific preferences for habitat features. Crested blenny and freckled blenny were recaptured at nest sites with significantly more oyster cover than nest sites occupied by striped blenny. Blennies occupied nest sites for several months and across annual breeding seasons suggesting continued residency within small areas of individual oyster reefs throughout their lives. Strong fidelity for reefs and nest sites potentially makes blennies more susceptible to disturbances than gobies, but both may be vulnerable to habitat disturbance at scales < 5 m. Thus, blennies and gobies may be useful indicator species for changes within estuarine habitats and ecosystems.

Abstract Very little is understood about the spawning habitat of endangered delta smelt Hypomesus transpacificus, which hinders ongoing recovery efforts such as wetland habitat restoration and spawning habitat augmentation. To address this, the spawning response of wild-caught H. transpacificus to different substrates and water velocities was examined across three experiments. In experiment 1, spawning response to dead wood, pebble, natural and artificial Schoenoplectus acutus, empty tray, and tank floor at water velocities of 1.4 and 8.8 cm/s was tested. Egg deposition on pebble at 8.8 cm/s velocity (78.1% of 7778 total eggs) was significantly greater than that on all other substrate-velocity combinations. In experiment 2, spawning response to natural S. acutus, dead wood, sand, pebble, cobble, and empty tray at velocities of 8.7 and 15.4 cm/s was tested. Egg deposition on pebble at 15.4 cm/s (61.5% of 36171 total eggs) was significantly greater than that on all substrate-velocity combinations except for sand at 15.4 cm/s. Sand at 15.4 cm/s (22.3%) contained significantly more eggs than all combinations except for pebble at 8.7 and 15.6 cm/s. In experiment 3, egg attachment to natural S. acutus, dead wood, sand, pebble, cobble, and empty tray when exposed to 14.6 cm/s velocity was tested. Egg loss on sand was significantly greater than that on empty tray and pebble, indicating that egg deposition on sand may have been underestimated in experiment 2. Together, these results indicate that H. transpacificus selects pebble and sand at higher water velocities for spawning under certain laboratory conditions. These findings are important, as they provide insight into the potential natural habitats that may be used for spawning and thereby inform ongoing habitat restoration efforts.

Abstract Recently, there has been much discussion about the role of the p-value in scientific research. The American Statistical Association has published an editorial that presents guidelines for the use and interpretation of p-values. Numerous authors have commented and criticized its use as a means to identify scientific importance of results and have called for an end to using the term “statistical significance.” Recent articles in Estuaries and Coasts were evaluated for reliance on the use of statistical significance and reporting errors were identified. Suggestions are made for improving what is reported related to statistical testing. Focus should be on scientific importance of estimates, estimation of the size of the effect and the certainty in the size of the effect instead of simply reporting a p-value and relying on hypothesis tests.

Abstract Juvenile summer flounder Paralichthys dentatus and southern flounder Paralichthys lethostigma exhibit ontogenetic segregation during spring and summer in southeastern USA estuaries, with summer flounder remaining primarily in polyhaline regions and southern flounder migrating to oligohaline habitat. To determine physicochemical conditions contributing to optimal nursery ground function for each species, growth rates, feeding rates, and gross growth efficiencies were examined in common-garden experiments at spring and summer thermohaline regimes. Experiments were conducted on young-of-the-year (45–100 mm total length; 0.9–8.9 g) summer flounder (15–25 °C, 10–30‰) and southern flounder (15–30 °C, 0–30‰) from North Carolina, and juvenile summer flounder from Delaware (15–25 °C, 30‰ only). Over the 15–25 °C and 10–30‰ conditions common to both species, means of all dependent variables were greater in summer flounder than southern flounder. Summer flounder grew best at 21–23 °C and 21–28‰. Low salinity (0–10‰) was physiologically suboptimal, especially at high (25 °C) summer temperatures. There was a significant direct effect of location (North Carolina vs Delaware) on growth efficiency of juvenile summer flounder, but not on growth rate, feeding rate, or linear growth rate. Growth potential of southern flounder was maximum at 25–26 °C and 10–30‰, and growth efficiency was highest at mesohaline salinities; yet growth was maintained at moderate levels over a broad range of oligohaline conditions, including ≤ 10‰, even at 30 °C. Differences in thermohaline conditions that affect growth potential illustrate spatiotemporal patterns and dynamics of optimal nursery potential for these two paralichthyid flounders.

Considerable efforts are underway to restore watersheds and estuaries downstream impacted by urban development; however, climate change (CC) may be undermining them. Current methods are limited in their ability to predict hydrology and water quality with CC and assess its effect on the efficiency of stormwater control measures (SCMs). We developed a method using downscaled global climate models (GCMs) from the Coupled Model Intercomparison Project Phase 5 (CMIP5) to project precipitation and temperatures; these were used to force a Storm Water Management Model (SWMM). Three scenarios, a historical and two Representative Concentration Pathways (RCP 4.5 and 8.5) with five GCMs, were used to produce ensemble results. All GCMs in both RCP scenarios projected increases in precipitation and temperature compared to historical conditions. Both RCPs exhibited their largest increases in precipitation, streamflow, total suspended solids (TSS), total nitrogen (TN), and total phosphorous (TP) loads in the winter, summer exhibited the largest increase in temperature. Median loads of TSS, TN, and TP increased 3.1%, 2.5%, and 9.9%, respectively, for RCP 4.5, and increased 3.8%, 3.1%, and 10.4%, respectively, for RCP 8.5. Median reductions in TSS, TN, and TP SCM efficiency for RCP 4.5 were projected to be 6%, 7%, and 11%, respectively; and 11%, 12%, and 17% for RCP 8.5, respectively. Thus, it is likely that additional efforts will be needed to meet water quality goals in the future. Methods such as these can help create climate resilient watershed improvement strategies and guide urban stormwater planning against likely future changes as a result of CC.

Anaerobic ammonium oxidation (anammox) is an important pathway for the removal of fixed nitrogen from aquatic and terrestrial ecosystems. Previous studies on anammox were focused on the surface sediments in estuaries, but the activity and community composition of anammox bacteria in the estuarine subsurface sediments remained unknown. In this study, we used high-throughput sequencing of 16S rRNA gene combined with 15N isotope tracing method to investigate the activity, diversity, and spatio-temporal distribution of anammox bacteria in sediment cores of the Pearl River Estuary (PRE). Our results indicated that anammox in the subsurface sediments has significant potential activity, contributing to approximately 17.49% of the total microbial nitrogen loss. A variety of anammox bacteria, including Candidatus Scalindua, Ca. Brocadia, Ca. Jettenia, and Ca. Kuenenia, were all detected in the subsurface sediments. Moreover, the anammox bacterial community had a significant specific geographic distribution but no obvious difference along the sediment depth. Multiple environmental factors including salinity, and NH4+ and NO3− contents, synergistically shaped the diversity and distribution of anammox bacteria in PRE sediments.

Floc size, density, and settling velocity were investigated in the Connecticut River estuary over 3 years spanning varying fluvial discharge regimes to determine the role of cohesive suspended particle characteristics in the sediment-transport patterns of an energetic estuary. Concurrent measurements of flow, bed stress, salinity, and suspended sediment concentration were used to identify primary controls on floc size variability. Water discharge ranged from 202 to 910 m3/s between the three sampling campaigns, and the timing of major sediment-discharge events preceding measurement periods from 23 to 162 days. Two distinct particle populations were observed under high and low sediment-discharge regimes. With abundant fluvial sediment input, flocculation occurred resulting in large, loosely packed flocs dominating the suspended signal (median sizes of 194–209 μm; median excess densities of 13–17 kg/m3). Following an extended period of low sediment discharge, small, dense aggregates resuspended from the bed were observed throughout the water column (median size of 171 μm and excess density of 60 kg/m3). The timing and partial decoupling of water and sediment discharge led to inter-annual patterns of particle packaging controlled by fresh sediment supply. When the estuary is “charged” with sediment following high discharge events, the characteristic large, less dense flocs with lower settling velocities primarily bypass the estuary. The similar disaggregated grain size distribution of the suspended material of the two regimes suggests the same source sediment is reintroduced to the estuary with the intrusion of the salt wedge, which extends farther up-estuary during low-discharge regimes. The fines repackaged as dense aggregates ultimately supply the channel margins and off-channel coves currently experiencing sediment accumulation.

Salem, MA, located north of Boston, has a rich, well-documented history dating back to settlement in 1626 CE, but the associated anthropogenic impacts on Salem Sound are poorly constrained. This project utilized dated sediment cores from the sound to assess the proxy record of anthropogenic alterations to the system and compared the proxy records to the known history. Proxies included bulk stable isotopes of organic matter, magnetic susceptibility, and trace metal concentrations. Our data reveal clear changes in organic matter composition and concentration associated with land use changes and twentieth century sewage disposal practices. Further, metals data correspond with local industrial activity, particularly the historic tanning industry in Peabody, MA. Although conservation practices of past decades have improved the state of Salem Sound, the stratigraphic record demonstrates that the environment is still affected by anthropogenic influences, and has not attained conditions consistent with pre-anthropogenic baseline. The approach and results of this study are applicable to coastal embayments that are being assessed for remediation, especially those with scant historic or monitoring data.

Seasonal responses in estuarine metabolism (primary production, respiration, and net metabolism) were examined using two complementary approaches. Total ecosystem metabolism rates were calculated from dissolved oxygen time series using Odum's open water method. Water column rates were calculated from oxygen-based bottle experiments. The study was conducted over a spring-summer season in the Pensacola Bay estuary at a shallow seagrass-dominated site and a deeper bare-bottomed site. Water column integrated gross production rates more than doubled (58.7 to 130.9 mmol O2 m-2 d-1) from spring to summer, coinciding with a sharp increase in water column chlorophyll-a, and a decrease in surface salinity. As expected, ecosystem gross production rates were consistently higher than water column rates, but showed a different spring-summer pattern, decreasing at the shoal site from 197 to 168 mmol O2 m-2 d-1 and sharply increasing at the channel site from 93.4 to 197.4 mmol O2 m-2 d-1. The consistency among approaches was evaluated by calculating residual metabolism rates (ecosystem - water column). At the shoal site, residual gross production rates decreased from spring to summer from 176.8 to 99.1 mmol O2 m-2 d-1, but were generally consistent with expectations for seagrass environments, indicating that the open water method captured both water column and benthic processes. However, at the channel site, where benthic production was strongly light-limited, residual gross production varied from 15.7 mmol O2 m-2 d-1 in spring to 86.7 mmol O2 m-2 d-1 in summer. The summer rates were much higher than could be realistically attributed to benthic processes, and likely reflected a violation of the open water method due to water column stratification. While the use of sensors for estimating complex ecosystem processes holds promise for coastal monitoring programs, careful attention to the sampling design, and to the underlying assumptions of the methods, is critical for correctly interpreting the results. This study demonstrated how using a combination of approaches yielded a fuller understanding of the ecosystem response to hydrologic and seasonal variability.

Numerical modeling has emerged over the last several decades as a widely accepted tool for investigations in environmental sciences. In estuarine research, hydrodynamic and ecological models have moved along parallel tracks with regard to complexity, refinement, computational power, and incorporation of uncertainty. Coupled hydrodynamic-ecological models have been used to assess ecosystem processes and interactions, simulate future scenarios, and evaluate remedial actions in response to eutrophication, habitat loss, and freshwater diversion. The need to couple hydrodynamic and ecological models to address research and management questions is clear, because dynamic feedbacks between biotic and physical processes are critical interactions within ecosystems. In this review we present historical and modern perspectives on estuarine hydrodynamic and ecological modeling, consider model limitations, and address aspects of model linkage, skill assessment, and complexity. We discuss the balance between spatial and temporal resolution and present examples using different spatiotemporal scales. Finally, we recommend future lines of inquiry, approaches to balance complexity and uncertainty, and model transparency and utility. It is idealistic to think we can pursue a "theory of everything" for estuarine models, but recent advances suggest that models for both scientific investigations and management applications will continue to improve in terms of realism, precision, and accuracy.

Upland areas of southeastern U.S. tidal creek watersheds are popular locations for development, and they form part of the estuarine ecosystem characterized by high economic and ecological value. The primary objective of this work was to define the relationships between coastal development, with its concomitant land use changes and associated increases in nonpoint source pollution loading, and the ecological condition of tidal creek ecosystems including related consequences to human populations and coastal communities. Nineteen tidal creek systems, located along the southeastern United States coast from southern North Carolina to southern Georgia, were sampled during summer, 2005 and 2006. Within each system, creeks were divided into two primary segments based upon tidal zoning: intertidal (i.e., shallow, narrow headwater sections) and subtidal (i.e., deeper and wider sections) and then watersheds were delineated for each segment. Relationships between coastal development, concomitant land use changes, nonpoint source pollution loading, the ecological condition of tidal creek ecosystems, and the potential impacts to human populations and coastal communities were evaluated. In particular, relationships were identified between the amount of impervious cover (indicator of coastal development) and a range of exposure and response measures including increased chemical contamination of the sediments, increased pathogens in the water, increased nitrate/nitrite levels, increased salinity range, decreased biological productivity of the macrobenthos, alterations to the food web, increased flooding potential, and increased human risk of exposure to pathogens and harmful chemicals. The integrity of tidal creeks, particularly the headwaters or intertidally-dominated sections, were impaired by increases in nonpoint source pollution associated with sprawling urbanization (i.e., increases in impervious cover). This finding suggests these habitats are valuable early warning sentinels of ensuing ecological impacts and potential public health and flooding risk from sprawling coastal development. Results also validate the use of a conceptual model with impervious cover thresholds for tidal creek systems in the southeast region.

The extent and temporal variability of denitrification activity was measured in Yaquina Bay, Oregon, over a year using sediment cores collected approximately monthly from August 2003 through August 31, 2004. Denitrification rates in sediments from a marine-dominated intertidal sand flat near the mouth of the estuary averaged 0.181 ±0.114 mmol m-2 d-1 whereas sediments in the estuary (5 stations) and river averaged 0.626 ±0.141 mmol m-2 d-1. Sediment cores from all estuarine sites indicated denitrification activity throughout the year and were within the values reported for other temperate estuaries. Denitrification rates decreased with depth from 0.4 mmol m-2 d-1 in the upper 2 to 5 cm of sediment to 0.006 mmol m-2 d-1 at 28 cm sediment depth, indicating denitrification occurred primarily in the upper 5 cm. There was no relationship between denitrification rate and nitrate concentrations in the overlying water column (r2 = 0.16). Denitrification rates were lowest in areas with low sediment carbon content, particularly in the sandy intertidal areas at the mouth of the estuary (r2 = 0.78). The results suggest that denitrification rates in this estuary were influenced primarily by the availability of organic carbon. The amount of nitrogen removed by denitrification was estimated to be 8.7 percent of the annual Yaquina River load for August 2003 through August 2004. The relatively low percent lost via denitrification may be due to high river discharge when the nitrogen load was greatest during winter storm events and dissolved nitrogen was exported directly from the estuary into the Pacific Ocean. Stable isotopes were used to investigate the carbon source. The carbon isotope data increased from -27 δ13C in the freshwater river to -21.5 δ13C at the seawater site, reflecting a typical change from terrestrial plant vegetation to phytoplankton carbon sources. Similar values for δ13C between suspended and benthic sediments indicated resuspension and mixing occurred during tidal inflow.

Vibrio species are marine bacteria that occur in estuaries worldwide; many are virulent human pathogens with high levels of antibiotic resistance. The average annual incidence of all Vibrio infections has increased by 41% between 1996 and 2005. V. vulnificus (Vv), a species associated with shellfish and occurring in the US Southeast, has ranges of temperature (16-33 °C) and salinity (5-20 ppt) dependencies for optimal growth. Increased water temperatures caused by atmospheric warming and increased salinity gradients caused by sea level rise raise concerns for the effect of climate change on the geographic range of Vv and the potential for increased exposure risk. This research combined monthly field sampling, laboratory analysis, and modeling to identify the current occurrence of Vv in the Winyah Bay estuary (South Carolina, USA) and assess the possible effects of climate change on future geographic range and exposure risk in the estuary. Vv concentrations ranged from 0 to 58 colony forming units (CFU)/mL, salinities ranged from 0 to 28 ppt, and temperature from 18 to 31 °C. A significant empirical relationship was found between Vv concentration and salinity and temperature that fit well with published optimal ranges for growth for these environmental parameters. These results, when coupled with an existing model of future specific conductance, indicated that sea level rise has a greater impact on exposure risk than temperature increases in the estuary. Risk increased by as much as four times compared to current conditions with the largest temporally widespread increase at the most upriver site where currently there is minimal risk.

Over the past decade, nitrogen (N) loads to Narragansett Bay have decreased by more than 50%. These reductions were, in large part, the direct result of multiple wastewater treatment facility upgrades to tertiary treatment, a process which employs N removal. Here we document ecosystem response to the N reductions and assess how the distribution of sewage N in Narragansett Bay has changed from before, during, and shortly after the upgrades. While others have observed clear responses when data were considered annually, our seasonal and regional comparisons of pre- and post-tertiary treatment dissolved inorganic nitrogen (DIN) concentrations and Secchi depth data, from bay-wide surveys conducted periodically from the early 1970s through 2016, resulted in only a few subtle differences. Thus we sought to use stable isotope data to assess how sewage N is incorporated into the ecology of the Bay and how its distribution may have changed after the upgrades. The nitrogen (δ15N) and carbon (δ13C) stable isotope measurements of particulate matter served as a proxy for phytoplankton, while macroalgae served as short-term integrators of water column bio-available N, and hard clams (Mercenaria mercenaria) as integrators of water column production. In contrast to other estuarine stable isotope studies that have observed an increased influence of isotopically lower marine N when sewage N is reduced, the opposite has occurred in Narragansett Bay. The tertiary treatment upgrades have increased the effluent δ15N values by at least 2‰. The plants and animals throughout Narragansett Bay have similarly increased by 1-2‰, on average. In contrast, the δ13C values measured in particulate matter and hard clams have declined by about the same amount. The δ15N results indicated that, even after the N-reductions, sewage N still plays an important role in supporting primary and secondary production throughout the Bay. However, the δ13C suggest that overall net production in Narragansett Bay has decreased. In the five years after the major wastewater treatment facilities came on-line for nutrient removal, oligotrophication has begun but sewage remains the dominant source of N to Narragansett Bay.

Depth of colonization (Zc ) is a useful seagrass growth metric that describes seagrass response to light availability. Similarly, percent surface irradiance at Zc (% SI) is an indicator of seagrass light requirements with applications in seagrass ecology and management. Methods for estimating Zc and % SI are highly variable making meaningful comparisons difficult. A new algorithm is presented to compute maps of median and maximum Zc , Zc, med and Zc,max , respectively, for four Florida coastal areas (Big Bend, Tampa Bay, Choctawhatchee Bay, Indian River Lagoon). Maps of light attenuation (Kd ) based on MODIS satellite imagery, PAR profiles, and Secchi depth measurements were combined with seagrass growth estimates to produce maps of % SI at Zc,med and Zc,max . Among estuary segments, mean Zc,med varied from (±s.e.) 0.80±0.13 m for Old Tampa Bay to 2.33±0.26 m for Western Choctawhatchee Bay. Standard errors for Zc,med were 1-10% of the segment means. Percent SI at Zc,med averaged 18% for Indian River Lagoon (range = 9-24%), 42% for Tampa Bay (37-48%) and 58% for Choctawhatchee Bay (51-75%). Estimates of % SI were significantly lower in Indian River Lagoon than in the other estuaries, while estimates for Tampa Bay and Choctawhatchee Bay were higher than the often cited estimate of 20%. Spatial gradients in depth of colonization and % SI were apparent in all estuaries. The analytical approach could be applied easily to new data from these estuaries or to other estuaries and could be incorporated routinely in assessments of seagrass status and condition.

A highly resolved, 3-d model of hydrodynamics and Alexandrium fundyense in an estuarine embayment has been developed to investigate the physical and biological controls on a recurrent harmful algal bloom. Nauset estuary on Cape Cod (MA, USA) consists of three salt ponds connected to the ocean through a shallow marsh and network of tidal channels. The model is evaluated using quantitative skill metrics against observations of physical and biological conditions during three spring blooms. The A. fundyense model is based on prior model applications for the nearby Gulf of Maine, but notable modifications were made to be consistent with the Nauset observations. The dominant factors controlling the A. fundyense bloom in Nauset were the water temperature, which regulates organism growth rates, and the efficient retention of cells due to bathymetric constraints, stratification, and cell behavior (diel vertical migration). Spring-neap variability in exchange altered residence times, but for cell retention to be substantially longer than the cell doubling time required both active vertical migration and stratification that inhibits mixing of cells into the surface layer by wind and tidal currents. Unlike in the Gulf of Maine, the model results were relatively insensitive to cyst distributions or germination rates. Instead, in Nauset, high apparent rates of vegetative cell division by retained populations dictated bloom development. Cyst germination occurred earlier in the year than in the Gulf of Maine, suggesting that Nauset cysts have different controls on germination timing. The model results were relatively insensitive to nutrient concentrations, due to eutrophic conditions in the highly impacted estuary or due to limitations in the spatial and temporal resolution of nutrient sampling. Cell loss rates were inferred to be extremely low during the growth phase of the bloom, but increased rapidly during the final phase due to processes that remain uncertain. The validated model allows a quantitative assessment of the factors that contribute to the development of a recurrent harmful algal bloom and provides a framework for assessing similarly impacted coastal systems.

In Narragansett Bay, light attenuation by total suspended sediments (TSS), colored dissolved organic matter (CDOM), and phytoplankton chlorophyll-a (chl-a) pigment is 129%, 97%, and 70%, respectively, of that by pure seawater. Spatial distribution of light attenuation indicates higher values in the upper Bay, where rivers with sediment and nutrient-rich waters enter and elevate TSS, CDOM, and chl-a concentrations. The temporal trends of light attenuation during the summer months (July-August) differed at various locations in the Bay, having the highest values in July. For the same period, spectral methods overestimated attenuation throughout the Bay. These findings quantify the behavior of light attenuation in space and time, providing information that can guide decisions related to improving water clarity and help understanding the effects of various environmental and management scenarios on it.

Sea level rise is causing shoreline erosion, increased coastal flooding, and marsh vulnerability to the impact of storms. Coastal marshes provide flood abatement, carbon and nutrient sequestration, water quality maintenance, and habitat for fish, shellfish, and wildlife, including species of concern, such as the saltmarsh sparrow (Ammodramus caudacutus). We present a climate change adaptation strategy (CCAS) adopted by scientific, management, and policy stakeholders for managing coastal marshes and enhancing system resiliency. A common adaptive management approach previously used for restoration projects was modified to identify climate-related vulnerabilities and plan climate change adaptive actions. As an example of implementation of the CCAS, we describe the stakeholder plans and management actions the US Fish and Wildlife Service and partners developed to build coastal resiliency in the Narrow River Estuary, RI in the aftermath of Superstorm Sandy. When possible an experimental BACI (Before-After, Control-Impact) design, described as pre- and post-sampling at the impact site and one or more control sites, was incorporated into the climate change adaptation and implementation plans. Specific climate change adaptive actions and monitoring plans are described, and include shoreline stabilization, restoring marsh drainage, increasing marsh elevation, and enabling upland marsh migration. The CCAS provides a framework and methodology for successfully managing coastal systems faced with deteriorating habitat, accelerated sea level rise, and changes in precipitation and storm patterns.

In southern New England, salt marshes are exceptionally vulnerable to the impacts of accelerated sea level rise. Regional rates of sea level rise have been as much as 50% greater than the global average over past decades: a more than four-fold increase over late-Holocene background values. In addition, coastal development blocks many potential marsh migration routes, and compensatory mechanisms relying on positive feedbacks between inundation and sediment deposition are insufficient to counter inundation increases in extreme low turbidity tidal waters. Accordingly, multiple lines of evidence suggest marsh submergence is occurring in southern New England. A combination of monitoring data, field re-surveys, radiometric dating, and analysis of peat composition have established that, beginning in the early and mid-twentieth century, the dominant low marsh plant, Spartina alterniflora, has encroached upwards in tidal marshes, and typical high marsh plants, including Juncus gerardii and Spartina patens have declined, providing strong evidence that vegetation changes are being driven, at least in part, by higher water levels. Additionally, aerial and satellite imagery show shoreline retreat, widening and headward extension of channels, and new and expanded interior depressions. Papers in this special section highlight changes in marsh-building processes, patterns of vegetation loss, and shifts in species composition. The final papers turn to strategies for minimizing and coping with marsh loss by managing adaptively and planning for landward marsh migration. It is hoped that this collection offers lessons that will be of use to researchers and managers on coasts where relative sea level is not yet rising as fast as in southern New England.

Numerous marine and terrestrial species have shifted their ranges poleward in response to warming from global climate change. However, few studies have examined range shifts of subtidal benthic communities in estuarine and nearshore waters. This study examined 20 years (1990-2010) of occurrence and abundance data of soft-bottom, benthic invertebrates along the Atlantic coast of the USA. Data from two biogeographic provinces (Carolinian and Virginian), which spanned 15° of latitude from mid-Florida to Cape Cod, were extracted from a national coastal assessment program. Mean water temperatures increased significantly during the study period, bottom water by 1.6 °C and surface water by 1.7 °C. Of 25 species with significant changes in centers of abundance (out of the 30 most prevalent), 18 (60%) shifted northward and 7 (23%) shifted southward. Species that shifted north moved an average distance of 181 km, in contrast with 65 km for species that shifted south. The southern limits of 22 species showed significant northward shifts; because there was little change in northern limits, this resulted in an average 25% range contraction. Community composition changed during the study period, most notably in southern latitudes. Five Carolinian species surmounted their northerly biogeographic boundary. Consequences of these range shifts include changes in benthic community structure and function, which have strong implications for ecosystem functioning and services including changes in fisheries dependent upon benthic prey.

Worldwide coral reef conditions continue to decline despite the valuable socio-economic benefits of these ecosystems. There is growing recognition that quantifying reefs in terms reflecting what stakeholders value is vital for comparing inherent tradeoffs among coastal management decisions. Terrestrial sediment runoff ranks high as a stressor to coral reefs and is a key concern in Puerto Rico where reefs are among the most threatened in the Caribbean. This research aimed to identify the degree to which sediment runoff impacts production of coral reef ecosystem services and the potential for watershed management actions to improve these services. Ecosystem service production functions were applied to map and translate metrics of ecological reef condition into ecosystem services production under a gradient of increasing sediment delivery. We found that higher sediment delivery decreased provisioning of most ecosystem services, including ecosystem integrity, bioprospecting discovery, and reef-based recreational opportunities and fisheries production. However shoreline protection and services with a strong contribution from non-reef habitats (e.g., mangroves, seagrasses) were higher in locations with high sediment delivery, although there was a strong inshore effect suggesting the influence of distance to shore, depth, and inshore habitats. Differences among services may indicate potential tradeoffs and the need to consider habitat connectivity, nursery habitat, accessibility, and sediment buffering. The relationships we have identified can be used to link stakeholder values to decision alternatives to ensure continued provisioning of these services and the well-being of communities.

Tidal salt marsh is a key defense against, yet is especially vulnerable to, the effects of accelerated sea level rise. To determine whether salt marshes in southern New England will be stable given increasing inundation over the coming decades, we examined current loss patterns, inundation-productivity feedbacks, and sustaining processes. A multi-decadal analysis of salt marsh aerial extent using historic imagery and maps revealed that salt marsh vegetation loss is both widespread, and accelerating, with vegetation loss rates over the past four decades summing to 17.3%. Seaward retreat of the marsh edge, widening and headward expansion of tidal channel networks, loss of marsh islands, and the development and enlargement of interior depressions found on the marsh platform contributed to vegetation loss. Inundation due to sea level rise is strongly suggested as a primary driver: vegetation loss rates were significantly negatively correlated with marsh elevation (r2=0.96; p=0.0038), with marshes situated below mean high water (MHW) experiencing greater declines than marshes sitting well above MHW. Growth experiments with Spartina alterniflora, the Atlantic salt marsh ecosystem dominant, across a range of elevations and inundation regimes further established that greater inundation decreases belowground biomass production of Spartina alterniflora and thus negatively impacts organic matter accumulation. These results suggest that southern New England salt marshes are already experiencing deterioration and fragmentation in response to sea level rise, and may not be stable as tidal flooding increases in the future.

Northeastern US salt marshes face multiple co-stressors, including accelerating rates of relative sea level rise (RSLR), elevated nutrient inputs, and low sediment supplies. In order to evaluate how marsh surface elevations respond to such factors, we used surface elevation tables (SETs) and surface elevation pins to measure changes in marsh surface elevation in two eastern Long Island Sound salt marshes, Barn Island and Mamacoke Marsh. We compare marsh elevation change at these two systems with recent rates of RSLR and find evidence of differences between the two sites; Barn Island is maintaining its historic rate of elevation gain (2.3± 0.24 mm yr-1 from 2003 to 2013) and is no longer keeping pace with RSLR, while Mamacoke shows evidence of a recent increase in rates (4.2 ± 0.52 mm yr-1 from 1994 to 2014) to maintain its elevation relative to sea level. In addition to data on short-term elevation responses at these marshes, both sites have unusually long and detailed data on historic vegetation species composition extending back more than half a century. Over this study period, vegetation patterns track elevation change relative to sea levels, with the Barn Island plant community shifting towards those plants that are found at lower elevations and the Mamacoke vegetation patterns showing little change in plant composition. We hypothesize that the apparent contrasting trend in marsh elevation at the sites is due to differences in sediment availability, salinity, and elevation capital. Together these two systems provide critical insight into the relationships between marsh elevation, high marsh plant community, and changing hydroperiods. Our results highlight that not all marshes in southern New England may be responding to accelerated rates of RSLR in the same manner.

Spatial variation in mercury (Hg) and methylmercury (MeHg) bioaccumulation in urban coastal watersheds reflects complex interactions between Hg sources, land use, and environmental gradients. We examined MeHg concentrations in fauna from the Delaware River estuary, and related these measurements to environmental parameters and human impacts on the waterway. The sampling sites followed a north to south gradient of increasing salinity, decreasing urban influence, and increasing marsh cover. Although mean total Hg in surface sediments (top 4cm) peaked in the urban estuarine turbidity maximum and generally decreased downstream, surface sediment MeHg concentrations showed no spatial patterns consistent with the examined environmental gradients, indicating urban influence on Hg loading to the sediment but not subsequent methylation. Surface water particulate MeHg concentration showed a positive correlation with marsh cover whereas dissolved MeHg concentrations were slightly elevated in the estuarine turbidity maximum region. Spatial patterns of MeHg bioaccumulation in resident fauna varied across taxa. Small fish showed increased MeHg concentrations in the more urban/industrial sites upstream, with concentrations generally decreasing farther downstream. Invertebrates either showed no clear spatial patterns in MeHg concentrations (blue crabs, fiddler crabs) or increasing concentrations further downstream (grass shrimp). Best-supported linear mixed models relating tissue concentration to environmental variables reflected these complex patterns, with species specific model results dominated by random site effects with a combination of particulate MeHg and landscape variables influencing bioaccumulation in some species. The data strengthen accumulating evidence that bioaccumulation in estuaries can be decoupled from sediment MeHg concentration, and that drivers of MeHg production and fate may vary within a small region.

This study evaluated the relative importance of the N arragansett Bay estuary (RI and MA, USA), and associated tidal rivers and coastal lagoons, as nurseries for juvenile winter flounder, Pseudopleuronectes americanus, and summer flounder, Paralichthys dentatus. Winter flounder (WF) and summer flounder (SF) abundance and growth were measured from May to October (2009-2013) and served as indicators for the use and quality of shallow-water habitats (water depth < 1.5-3.0 m). These bioindicators were then analyzed with respect to physiochemical conditions to determine the mechanisms underlying intra-specific habitat selection. WF and SF abundances were greatest in late May and June (maximum monthly mean = 4.9 and 0.55 flounder/m2 for WF and SF, respectively), and were significantly higher in the tidal rivers relative to the bay and lagoons. Habitat-related patterns in WF and SF abundance were primarily governed by their preferences for oligohaline (0.1-5 ppt) and mesohaline (6-18 ppt) waters, but also their respective avoidance of hypoxic conditions (< 4 mg DO/L) and warm water temperatures (> 25 °C). Flounder habitat usage was also positively related to sediment organic content, which may be due to these substrates having sufficiently high prey densities. WF growth rates (mean = 0.25 ± 0.14 mm/d) were negatively correlated with the abundance of conspecifics, whereas SF growth (mean = 1.39 ± 0.46 mm/d) was positively related to temperature and salinity. Also, contrary to expectations, flounder occupied habitats that offered no ostensible advantage in intra-specific growth rates. WF and SF exposed to low salinities in certain rivers likely experienced increased osmoregulatory costs, thereby reducing energy for somatic growth. Low-salinity habitats, however, may benefit flounder by providing refugia from predation or reduced competition with other estuarine fishes and macro-invertebrates. Examining WF and SF abundance and growth across each species' broader geographic distribution revealed that southern New England habitats may constitute functionally significant nurseries. These results also indicated that juvenile SF have a geographic range extending further north than previously recognized.